Provided by: toppic_1.5.3+dfsg1-1build3_amd64 bug

NAME

       topmg - Top-down mass spectrometry based proteoform identification using Mass Graphs

SYNOPSIS

          topmg [options] database-file-name spectrum-file-names

DESCRIPTION

       TopMG  (Top-down mass spectrometry based proteoform identification using Mass Graphs) is a
       software tool for identifying ultra-modified proteoforms by searching top-down tandem mass
       spectra against a protein sequence database. It is capable of identifying proteoforms with
       multiple variable PTMs  and  unexpected  alterations,  such  as  histone  proteoforms  and
       phosphorylated   ones.   It  uses  mass  graphs,  which  efficiently  represent  candidate
       proteoforms with multiple  variable  PTMs,  to  increase  the  speed  and  sensitivity  in
       proteoform  identification.  In addition, approximate spectrum-based filtering methods are
       employed for protein sequence filtering, and a Markov chain Monte Carlo  method  (TopMCMC)
       is used for estimating the statistical significance of identifications.

       1. Input

             • A protein database file in the FASTA format

             • A mass spectrum data file in the msalign format

             • A text file of variable PTMs

             • A text file of fixed PTMs (optional)

             • A text file containing LC/MS feature information (optional)

       2. Output

       TopMG  outputs  two  csv files, an xml file, and a collection of html files for identified
       proteoforms. For example, when the input mass spectrum data file  is  spectra_ms2.msalign,
       the output includes:

          • spectra_ms2_topmg_prsm.csv: a csv file containing identified PrSMs with an E-value or
            spectrum level FDR cutoff.

          • spectra_ms2_topmg_proteoform.csv: a csv file containing identified  proteoforms  with
            an E-value or proteoform level FDR cutoff.

          • spectra_ms2_topmg_proteoform.xml:  an xml file containing identified proteoforms with
            the E-value or proteoform level FDR cutoff.

          • spectra_html/topmg_prsm_cutoff: a folder containing java script files  of  identified
            PrSMs using the E-value or spectrum level FDR cutoff.

          • spectra_html/topmg_proteoform_cutoff:  a  folder  containing  java  script  files  of
            identified PrSMs using the E-value or proteoform level cutoff.

          • spectra_html/topview: a  folder  containing  html  files  for  the  visualization  of
            identified PrSMs.

       To  browse  identified  proteins, proteoforms, and PrSMs, use a chrome browser to open the
       file spectra_html/topview/index.html. Google Chrome is recommended (Firefox,  IE  are  not
       recommended).

       When  the  input  contains two or more spectrum files, TopMG outputs two csv files, an xml
       file, and a collection of html files for each input file. When a file  name  is  specified
       for  combined identifications, it combines spectra and proteoforms identified from all the
       input files, removes redundant proteoform identifications, and reports two csv  files,  an
       xml  file,  and a collection of html files for the combined results. For example, when the
       input is spectra1_ms2.msalign and spectra2_ms2.msalign and the combined output  file  name
       is "combined," the output files are:
          combined_ms2_topmg_prsm.csv:  a csv file containing PrSMs identified from all the input
          files with an E-value or spectrum level FDR cutoff.  combined_ms2_topmg_proteoform.csv:
          a  csv  file containing proteoforms identified from all the input files with an E-value
          or  proteoform  level  FDR  cutoff.   combined_ms2_topmg_proteoform.xml:  an  xml  file
          containing  proteoforms  identified  from  all  the  input  files  with  the E-value or
          proteoform level FDR cutoff.  combined_html/topmg_prsm_cutoff: a folder containing java
          script files of PrSMs identified from all the input files using the E-value or spectrum
          level FDR cutoff.   combined_html/topmg_proteoform_cutoff:  a  folder  containing  java
          script  files  of  PrSMs  identified  from  all  the  input  files using the E-value or
          proteoform level cutoff.  combined_html/topview: a folder containing html files for the
          visualization of identified PrSMs.

OPTIONS

       -h [ --help ] Print the help message.

       -a  [  --activation ] <CID|HCD|ETD|UVPD|FILE> Fragmentation method of tandem mass spectra.
       When FILE is used, fragmentation methods of spectra are given in the input  spectral  data
       file. Default value: FILE.

       -f  [  --fixed-mod  ]  <C57|C58|a  fixed modification file> Set fixed modifications. Three
       available options: C57, C58, or the name of a text  file  specifying  fixed  modifications
       (see  an example file). When C57 is selected, carbamidomethylation on cysteine is the only
       fixed modification. When C58 is selected, carboxymethylation on cysteine is the only fixed
       modification.

       -n  [  --n-terminal-form  ]  <a  list of allowed N-terminal forms> Set N-terminal forms of
       proteins.  Four  N-terminal  forms  can  be  selected:  NONE,  NME,  NME_ACETYLATION,  and
       M_ACETYLATION.  NONE  stands for no modifications, NME for N-terminal methionine excision,
       NME_ACETYLATION for N-terminal acetylation after the initiator methionine is removed,  and
       M_ACETYLATION for N-terminal methionine acetylation. When multiple forms are allowed, they
       are separated by commas. Default value: NONE,M_ACETYLATION,NME,NME_ACETYLATION.

       -d [ --decoy ] Use a shuffled decoy protein database to estimate spectrum  and  proteoform
       level  FDRs.  When  -d is chosen, a shuffled decoy database is automatically generated and
       appended to the target database before database search, and FDR rates are estimated  using
       the target-decoy approach.

       -e  [  --mass-error-tolerance ] <a positive integer> Set the error tolerance for precursor
       and fragment masses in ppm. Default value: 15.

       -p [ --proteoform-error-tolerance ] <a  positive  number>  Set  the  error  tolerance  for
       identifying PrSM clusters (in Dalton). Default value: 1.2 Dalton.

       -M  [  --max-shift  ] <a number> Set the maximum absolute value for unexpected mass shifts
       (in Dalton). Default value: 500.

       -t [ --spectrum-cutoff-type  ]  <EVALUE|FDR>  Set  the  spectrum  level  cutoff  type  for
       filtering PrSMs. Default value: EVALUE.

       -v [ --spectrum-cutoff-value ] <a positive number> Set the spectrum level cutoff value for
       filtering PrSMs. Default value: 0.01.

       -T [ --proteoform-cutoff-type ] <EVALUE|FDR> Set the  proteoform  level  cutoff  type  for
       filtering proteoforms and PrSMs. Default value: EVALUE.

       -V [ --proteoform-cutoff-value ] <a positive number> Set the proteoform level cutoff value
       for filtering proteoforms and PrSMs. Default value: 0.01.

       -i [ --mod-file-name ] <a modification file> Specify a text file of variable PTMs. See  an
       example file.

       -u  [  --thread-number  ]  <a  positive  number>  Set  the  number  of threads used in the
       computation. Default value: 1. The maximum number of threads is determined by the CPU  and
       memory  of  the  computer  used  for  computation.  About 4 GB memory is required for each
       thread. If the computer has 16 GB memory and a CPU with 8 cores,  the  maximum  number  of
       threads is 4 because 16 GB memory is required for 4 threads.

       -x  [  --no-topfd-feature  ]  Specify that there are no TopFD feature files for proteoform
       identification.

       -D [ --use-asf-diagonal ] Use the ASF-DIAGONAL method for protein sequence filtering.  The
       default  filtering  method  is  ASF-RESTRICT.  When  -D is selected, both ASF-RESTRICT and
       ASF-DIAGONAL will be used. The combined approach may identify more PrSMs, but it  is  much
       slower than using ASF-RESTRICT only. See this paper for more details.

       -P  [  --var-ptm  ]  <a positive number> Set the maximum number of variable PTM sites in a
       proteoform. Default value: 5.

       -s [ --num-shift <0|1|2> Set the maximum number of unexpected mass shifts in a proteoform.
       Default value: 0.

       -c  [  --combined-file-name  ]  <a  filename>  Specify  an  output  file name for combined
       identifications when the input consists of multiple spectrum files.

       -k [ --keep ] Keep intermediate files generated by TopMG.

ADVANCED OPTIONS

       -j [ --proteo-graph-dis ] <a positive number>  Set  the  length  of  the  largest  gap  in
       constructing proteoform graphs. Default value: 40. See this paper for more details.

       -G  [  --var-ptm-in-gap ] <a positive number> Set the maximum number of variable PTM sites
       in a gap in a proteoform graph. Default value: 5. See this paper for more details.

EXAMPLES

       To use the following examples, a  variable  modification  file  variable_mods.txt  in  the
       current foler is needed. (See an example.)

       • Search a deconvoluted MS/MS spectrum file spectra_ms2.msalign against a protein database
         file proteins.fasta with feature files. The user does not need to  specify  the  feature
         file  name. TopMG will automatically obtain the names of feature files from the spectrum
         file name spectra_ms2.msalign.

         topmg -i variable_mods.txt proteins.fasta spectra_ms2.msalign

       • Search   two   deconvoluted    MS/MS    spectrum    files    spectra1_ms2.msalign    and
         spectra2_ms2.msalign  against a protein database file proteins.fasta with feature files.
         In addition, all identifications are combined and reported using a file name "combined."

         topmg   -i   variable_mods.txt   -c   combined    proteins.fasta    spectra1_ms2.msalign
         spectra2_ms2.msalign

       • Search  all  deconvoluted  MS/MS  spectrum files in the current folder against a protein
         database file proteins.fasta with feature files.

         topmg -i variable_mods.txt proteins.fasta *_ms2.msalign

       • Search a deconvoluted MS/MS spectrum file spectra_ms2.msalign against a protein database
         file proteins.fasta without feature files.

         topmg -i variable_mods.txt -x proteins.fasta spectra_ms2.msalign

       • Search a deconvoluted MS/MS spectrum file spectra_ms2.msalign against a protein database
         file proteins.fasta with feature files and a fixed modification: carbamidomethylation on
         cysteine.

         topmg -i variable_mods.txt -f C57 proteins.fasta spectra_ms2.msalign

       • Search a deconvoluted MS/MS spectrum file spectra_ms2.msalign against a protein database
         file proteins.fasta  with  feature  files.  In  an  identified  proteoform,  at  most  1
         unexpected  mass  shift  and  4  variable  PTMs  are  allowed  and the maximum value for
         unexpected mass shifts is 10,000 Dalton.

         topmg -i variable_mods.txt -P 4 -s 1 -M 10000 proteins.fasta spectra_ms2.msalign

       • Search a deconvoluted MS/MS spectrum file spectra_ms2.msalign against a protein database
         file  proteins.fasta  with feature files. The error tolerance for precursor and fragment
         masses is 5 ppm.

         topmg -i variable_mods.txt -e 5 proteins.fasta spectra_ms2.msalign

       • Search a deconvoluted MS/MS spectrum file spectra_ms2.msalign against a protein database
         file  proteins.fasta  with  feature  files.  Use  the  target  decoy approach to compute
         spectrum level and proteoform level FDRs, filter identified proteoform  spectrum-matches
         by  a  5% spectrum level FDR, and filter identified proteoforms by a 5% proteoform level
         FDR.

         topmg  -i  variable_mods.txt  -d  -t  FDR  -v  0.05  -T  FDR  -V   0.05   proteins.fasta
         spectra_ms2.msalign

       • Search a deconvoluted MS/MS spectrum file spectra_ms2.msalign against a protein database
         file proteins.fasta with feature files. Use 6 CPU threads to speed up  the  computation.
         About 24 GB memory is required for 6 threads. If the computer lacks enough memory, TopMG
         may crash.

         topmg -i variable_mods.txt -u 6 proteins.fasta spectra_ms2.msalign

SEE ALSO

       • topfd (1)

       • toppic (1)

       • topdiff (1)

MAN PAGE PRODUCTION

       This man page was written by Filippo Rusconi <lopippo@debian.org>. Material was taken from
       http://proteomics.informatics.iupui.edu/software/toppic/manual.html.

AUTHOR

       Filippo  Rusconi  <lopippo@debian.org>  and  upstream  authors  (Dr.  Xiaowen Liu's Lab at
       Indiana University-Purdue University Indianapolis and others)

COPYRIGHT

       Filippo Rusconi and Indiana University-Purdue University Indianapolis